Good to hear its solved. The pulse width at one time, I believe, could only be set 1 to 5 but it was increased to 15 at one point and the labeling never changed. Previously if 5 was not enough for your drive you would have to enable Sherline mode which sets it to 40. However that mode is only possible at 25KHz kernel (1 second/ 25KHz = 40uS) so if you needed more than 5 and were also needing a higher kernel then you couldnt get it.
Now your issue, not sure why it had changed from the old to the new but could have just been you made a new profile at some point, possibly when you upgraded Mach versions it got set lower or possibly.... well who knows
Why it only affects the Y and not the rest is likely just down to the Y axis drives electronics being a bit slow on seeing the inputs so it needs the wider pulse could even be your breakout board on certain pins.
Doesnt really matter I suppose as long as its now working
Hood